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Coccolithophores play an important role in regulating the climate through their influence on the organic and inorganic carbon pumps. Coccolithophores' influence on the ocean carbon pumps depends on their ecology, our understanding of which is currently limited to a few species. My thesis thus aims at improving our knowledge of coccolithophore ecology by investigating the nature and function of the coccolithophore life cycle (haploid versus diploid phases) and quantifying the global standing stocks of the most common coccolithophore species. I used a trait-based framework and a multidisciplinary approach that combines statistical analysis, lab experiments, machine learning and numerical modelling. Using statistical analysis, I quantify the niche occupied by haploid and diploid coccolithophores, showing that the coccolithophore life cycle expands coccolithophore niche by ≈ 18%. Additionally, using lab experiments and numerical modelling, I demonstrate that a trade-off between nutrient storage and maximum growth is a critical bottom-up control of Coccolithus pelagicus life stages' distribution. Finally, using machine learning approaches, I estimate that two genera account for the majority of coccolithophore's global organic carbon standing stock and that mid-to-low latitude regions contribute similarly to high-latitude regions. This thesis provides novel insights into the ecology of the coccolithophore life cycle and the species that dominate coccolithophore biomass, and furthermore lays the groundwork for future coccolithophore research by identifying some of the key coccolithophore species and traits. My thesis also successfully applied novel multidisciplinary approaches leading the way to improve the ecology of marine plankton in general.

Northeastern Minnesota, like other regions, has exhibited recent climate change effects; predicted changes over the next century include longer dry periods, less snow accumulation, and more large rain and snow events. Carbonate system variables including pH, total inorganic carbon (TIC) concentrations, and total alkalinity (TA) are all highly dependent on and have feedbacks with these climate factors. These variables can also influence the quality of life for various species, such as trout, which rely on many streams along the north shore of Lake Superior for spawning habitats. Therefore, studying the current conditions of waterbodies in northeastern Minnesota is crucial for setting a baseline to estimate and predict the potential ramifications of regional climate change. Amity Creek, Tischer Creek, and the St. Louis River are three tributaries of Lake Superior varying in watershed size and overall length. This study investigated how pH, TA, and TIC of these tributaries are affected by seasonality, stormflow, and diurnal conditions, as well as their inter-annual variability based on available data. Seasonal sampling showed that carbonate system variables were relatively stable throughout fall before decreasing to minimum levels in spring when large freshets and rainfall events occurred. Carbonate system variables reached maximum levels in the summer when water and air temperatures were greatest in the sampling period and photosynthetic activity levels were also likely the highest. Autumn levels were similar to summer levels. During storm events, pH, TIC, and TA decreased compared to baseflow. Specific trends during storms were dependent on storm length, total precipitation, and prior precipitation amounts. Over a diurnal period in Amity Creek, pH increased during the morning hours to a midday maximum and then decreased. TIC and TA increased throughout the day, likely due to the increased influence of groundwater as the stream recovered from a rain event that occurred 4 days prior. Historically, pH has been increasing in Amity Creek and the St. Louis River, while Tischer Creek shows no trend. However, Tischer Creek and Amity Creek appear highly susceptible to inter-annual variability. Alkalinity trends were more difficult to assess due to data availability. However, where available, alkalinity trends closely follow the pH trends in the case of Amity Creek, while in the St. Louis River, alkalinity remained constant. In Tischer Creek, hardness data was used as a proxy variable for alkalinity. Hardness levels appeared to be increasing but had notably similar inter-annual variability as pH. This study demonstrates how carbonate system variables in streams and rivers can shift over long temporal scales, but more importantly how much variability can occur over the course of storm events and hours.

Impaired drainage from active and abandoned mines degrades the water quality of receiving streams and aquifers. Coal mine drainage (CMD) has been studied for decades in Appalachia, but unknowns and uncertainties are still present, including the influence of mine hydrogeology on the outflow chemistry of above-drainage mines. To evaluate the influence of recharge type on above-drainage mine chemistry, samples were collected every two weeks at a CMD outflow treatment system in Harrison County, West Virginia. Samples were collected to measure geochemical changes taking place in the mine workings and along the flowpath of the passive treatment system. Samples were divided into two groups based on the dominant type of recharge entering the mine during sample collection. Direct recharge dominated samples had lower concentrations of hydrolysable cations at the mine outflow, causing the discharge to be both net-acidic and net-alkaline during the study period. Total rare earth element concentrations at the outflow were positively correlated to Fe, Al, and Mn, and negatively correlated to pH and discharge. During both recharge regimes, Fe, Al, Mn, and rare earth elements were removed along the treatment system flowpath. Throughout the study period, 89% of dissolved inorganic carbon in the system was degassed to the atmosphere as CO2. This study demonstrates that varied recharge mechanisms can influence the CMD outflow chemistry, with implications in treatment system design, interpretation of routine chemical data, and extrapolation of CO2 efflux from CMD outflows for large-scale carbon balance studies.

The aim of this study was to enhance a vertical rotating membrane system that induced gas to liquid mass transfer, and to evaluate its performance by quantifying its inorganic carbon formation rate under different parameters such as carbon dioxide concentration in air, membrane's rotational speed and the composition of the liquid medium. In addition to that, the ability of the zinc plated and nickel wire meshes to catalyze the hydration reaction of carbon dioxide was tested in this study using a bench scale rotating membrane system. The system was enhanced by replacing the mechanism that rotated the mass transfer membrane mesh by a simpler mechanism which depended on rollers to rotate the membrane mesh. Testing the enhanced system indicated that increasing the carbon dioxide concentration from 1% to 2%, from 1% to 10% and from 2% to 10% increased the system’s inorganic carbon formation rate within the ranges of 69%-83%, 385%-521% and 179%-240% respectively. Furthermore, increasing the membrane’s rotational speed from 70 rpm to 90 rpm resulted in increasing the inorganic carbon formation rate within a percentage range of 27%-38%. Also, the tests showed that using BG-11 as a test medium instead of DI water increased the inorganic carbon formation rate within a percentage range of 27%-33.3% when testing the rotating membrane system under 1% and 2% carbon dioxide concentrations respectively. Also, an increase of 7% was noticed when BG-11 medium was used as a medium instead of DI water under 10% carbon dioxide concentration in air. Moreover, results showed that using zinc plated and nickel wire meshes had no impact on catalyzing the carbon dioxide hydration reaction.

Ribulose Bisphosphate Carboxylase/Oxygenase (Rubisco) is the central enzyme of the Calvin-Benson-Bassham (CBB) cycle and the most abundant enzyme on Earth. Nearly all carbon enters the biosphere via Rubisco carboxylation, yet no Rubisco has a maximum carboxylation rate above 15 /s and all Rubiscos catalyze a competing oxygenation of their five-carbon substrate. Evolution seems to have overcome this problem by selecting for CO2 concentrating mechanisms (CCMs) that place Rubisco in compartments where CO2 is highly concentrated. Distinct families of CCMs are found among bacteria, algae and plants, but they all function by elevating CO2 to promote carboxylation and inhibit oxygenation by Rubisco. Cyanobacteria are the ancestors of all green photosynthetic lineages, including plant chloroplasts, and have a CCM that requires a large (> 200 MDa) proteinaceous organelle called the carboxysome. Carboxysomes are composed of 10,000 proteins and encapsulate 2000 Rubisco active sites. Although present-day atmosphere is rich in O2 (21%) and CO2-poor (0.04%), cyanobacteria use the CCM to grow robustly in air. Mutations to the CCM abrogate air growth and are only rescued by markedly elevated CO2. By contrast, few plant species have CCMs. Land plants with CCMs, such as maize, are particularly productive, but no plant CCMs resemble those in bacteria. These considerations raise the prospect that engineering plants to express bacterial CCMs might improve their growth. Motivated by these questions, I use complementary experimental, informatic and modeling approaches to study the evolution and function of the bacterial CCM.I first perform a meta-analysis of the kinetic properties of 300 distinct Rubiscos and show that carboxylation and oxygenation are inextricably linked: increasing carboxylation efficiency entails an equal increase to oxygenation efficiency, suggesting that oxygenation cannot be avoided by mutating Rubisco itself. Second, by mathematical modeling I show that the 20 known components of the bacterial CCM are sufficient to concentrate CO2 and promote fast carboxylation in silico. As pH has wide-ranging effects on inorganic carbon chemistry, I also demonstrate that pH must be considered for CCM models to produce plausible results matching physiological measurements of cyanobacteria.To confirm that the CCM is formed of a small number of genes, I designed a high-throughput genetic screen in the chemotrophic bacterium H. neapolitanus. This screen identified 20 genes in 3 operons directly involved in the H. neapolitanus CCM, including a novel class of inorganic carbon transporters I term "DABs." To test whether these genes are sufficient for CCM function, I developed a Rubisco-dependent E. coli strain, CCMB1, whose growth reports on CCM function in vivo. CCMB1 only grows in minimal media when Rubisco is expressed, and only under elevated CO2 (> 20x ambient). I found that expression of the H. neapolitanus CCM genes permits CCMB1 growth in ambient air, thereby establishing a facile system for testing the contributions of individual genes to the functioning of the bacterial CCM.

The advent of global warming due to anthropogenic forcing has increased awareness of the global carbon cycle. The removal of CO2 from the atmosphere occurs via silicate and carbonate mineral weathering and this CO 2 is trapped when carbonate is re-precipitated in the ocean. Only silicate weathering creates a net sink for CO2, while carbonate weathering provides a short-term drawdown on the scale of decades to thousands of years. Silicate mineral dissolution rates however are on the order of thousands to millions of times slower than carbonate mineral weathering. On a human time scale (hundreds of years), the weathering of carbonate minerals may play an important role in the regulation of anthropogenic CO2. Increased atmospheric CO2 will influence dissolved inorganic carbon (DIC) within global rivers, via the enhancement of mineral weathering. Carbonate mineral solubility in physically open weathering environments is proportional to soil Pco2; so carbonate-weathering intensities should be affected by land use and soil thickness. To understand the ramifications of increased DIC in rivers, it is imperative to understand watershed scale processes that control and regulate the dissolved inorganic carbon cycle within watersheds. This dissertation investigates the fundamental controls on the acquisition, cycling, and transport of DIC from forested temperate carbonate bearing watersheds in Michigan and Slovenia. These investigations have culminated in an extensive database on ground and river waters that is used to further the understanding of carbonate weathering and DIC fluxes from watersheds. Watersheds with thicker soils are able to reach greater HCO3 - concentrations, than watersheds with thinner soils. Higher mean annual precipitation in Slovenia allows the Slovenian watersheds to have significantly higher HCO3- and Mg2+ weathering intensities than the Michigan watersheds. In some cases carbonate back precipitation is occurring within the watershed due to high calcite saturation states in the stream waters. Comparing the volume of carbonate removed from the watershed to the flux of dissolved inorganic carbon from the watershed indicates that back precipitation is negligible in the overall DIC flux from the watershed. Both calcite and dolomite weathering contribute to the DIC flux. In Slovenia, dolomite weathering is contributing approximately half the HCO3- flux from the watershed.

The sediment at both surface and one-foot depths in cores from the Gulf of Mexico, Mustang Island, and Corpus Christi Bay Texas, was analyzed by a wet combustion method to determine the per cent of carbon by dry weight in the organic fraction (organic carbon) and in the carbonate fraction (inorganic carbon). The statistical "t" test showed a significant difference (P = 0.05) between the mean per cent organic carbon content of the surface sediments from 1) Gulf (0.52%) and island (0.17%) and 2) island (0.17%) and bay (0.58%) and of one-foot sediments from 1) Gulf (0.29%) and island (0.11%) and 2) island (0.11%) and bay (0.44%). A significant difference was also found between the means of the per cent of carbonate carbon in surface sediments from 1) Gulf (0.50%) and island (0.09%) and 2) island (0.09%) and bay (0.68%) and in sediments from Gulf (0.32%) and bay (0.68%). A comparison of the means of the per cent of carbonate carbon in sediments at the surface (0.50%) and one-foot depths (0.32%) of all Gulf cores showed a significant difference at the 0.05 probability level. The organic carbon and inorganic carbon content of the sediment may be useful in distinguishing between Gulf and barrier island, and bay and barrier island sediments in the geologic record, but probably not for distinguishing between Gulf and bay environments